I used to hire at a startup. Following are the things I usually looked at. These are not sorted by severity, some are red flags but others are just irrelevant.
* not following instruction in the job advert
* CC resume to many recipients
* weird sender name in email
* compressed resume
* begging for job in the cover letter
* photo
* "career objective"
* personal information
* broken links
* clear lack of personalization in the resume format
* irrelevant background/experience
* inactive github profile (only uploaded projects etc.)
* MS Office skills
* acknowledgement, signature